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PhD Prep

Tuesday 22 March

So, I’m not currently enrolled and I’ve not received an offer yet as the graduate research office is inundated with paperwork atm, but I am going to start anyway as my commencement date was yesterday. I came in though and the only really did a few clerical things and taught for the afternoon (god it felt good to be back int he teaching labs 🙂), but after a quick chat with Peter I think I know what I need to be doing…

Read Read Read

It’s such a mammoth task to think about I feel like a decent methodology would be to:

  1. Start by reviewing my honours thesis
    • Go over the IL notes that I put aside when my project pivoted
    • Review some key papers that I identified in that work
  2. Start exploring the field more broadly
    • What are the papers that I didn’t get around to properly digesting?
    • What are some larger reviews that I really need to have read?
    • I have a big pile of papers in my “to read” list that I should probably down
  3. To try and read more broadly as well to get a more diverse understanding of the field

I really need to find a good way to be able to keep track of notes though as this is going to explode in detail so much. Perhaps I need a structure on this website to deal with that

What I actually did:

  • Chatted, got into the groove of things and decided to switch from Mendeley to Zotero for organisational reasons
  • Comment from Katya:

“At the moment you need to focus on literature covering the prediction of kinetics from MD simulations or ab initio MD simulations.”

Wednesday 23 March

What I actually did:

  • Today I really just focused on the CHM3911 tutorial and prep. I did also set up a self hosted WebDav server on my little NUC in order to save myself $20 USD on the Zotero storage access, which was ultimately decided by experiencing how incredibly slow Zotero’s paper storage is. Simply put, I can’t justify spending that money to wait for minutes for a 3 MB paper to download.

Friday 1 April


Well, It looks like the direction for my PhD has changed drastically after a chat with Katya, which means that I’m starting from scratch.

Meeting Notes

  • Lit review should be no more than 15 pages and the talk should be max 20 mins with a goal of 15 mins. These should focus on snippets of what is already out there in the field.
  • After much back and forth the new project is going to be something relating to better handling of solvation for UV-vis/Fluorescence spectroscopic predictions by utilising multilayered computational approaches

    • Could potentially involve a mix of QM/QM/SE/MM or any combination of theories to better model the solvent effects.
    • In contrast to the previous project, this will be far more focused on the application of pre-existing methodologies in new ways, as opposed to the creation of all new methods.
  • Potential search terms:

    • Excited state calculations
    • UV-Vis spectroscopic methods (QM, MD, etc.)
      • Predicting these in solvent (explicit, implicit, QM/MM)
    • Chromophores/fluorophores
    • Potential investigation; Green Fluorescent Protein (GFP)
  • Literature questions to ask?

    • What stops people from predicting chromophores and fluoropohres of interest?
    • What systems do they want to be able to predict? (avoid NDIs…)
  • Researchers of interest:

    • Martin Head-Grodon
    • Theresa Head-Gordon
    • Benedetta Mennicci
  • Emails to send:

    • Toby - seems like a potential co-supervisor, will know more about grand challenges in fluorescence and some ideal fluorophores to investigate
    • Rico - to postpone the allocation of a panel
    • Tanja - Seems like there may be an interesting side project here to generate a whole bunch of rate constants of radical polymerisation for machine learning purposes

The new project will likely be looking into something along the lines of multilayered (ONIOM-like) approaches to try and better account for solvent effects in excited state calculations, probably for better/more robust determination of fluorosence spectroscopy. This is going to take a lot of reading to get my head around...

Many papers have been found… now to read!